# UMLS::Similarity::nam.pm
#
# Module implementing the semantic similarity measure described
# by Nguyen and Al-Mubaid (2006)
#
# Copyright (c) 2004-2011,
#
# Bridget T McInnes, University of Minnesota, Twin Cities
# bthomson at cs.umn.edu
#
# Siddharth Patwardhan, University of Utah, Salt Lake City
# sidd at cs.utah.edu
#
# Serguei Pakhomov, University of Minnesota, Twin Cities
# pakh002 at umn.edu
#
# Ted Pedersen, University of Minnesota, Duluth
# tpederse at d.umn.edu
#
# Ying Liu, University of Minnesota
# liux0935 at umn.edu
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to
#
# The Free Software Foundation, Inc.,
# 59 Temple Place - Suite 330,
# Boston, MA 02111-1307, USA.
package UMLS::Similarity::nam;
use strict;
use warnings;
use UMLS::Similarity;
use UMLS::Similarity::ErrorHandler;
use vars qw($VERSION);
$VERSION = '0.07';
my $debug = 0;
my $originaloption = undef;
sub new
{
my $className = shift;
my $interface = shift;
my $params = shift;
return undef if(ref $className);
if($debug) { print STDERR "In UMLS::Similarity::nam->new()\n"; }
my $self = {};
# Bless the object.
bless($self, $className);
# The backend interface object.
$self->{'interface'} = $interface;
# check the configuration file if defined
my $errorhandler = UMLS::Similarity::ErrorHandler->new("nam", $interface);
if(!$errorhandler) {
print STDERR "The UMLS::Similarity::ErrorHandler did not load properly\n";
exit;
}
# check if the original distance score should be returned rather
# than the similarity score
if(defined $params->{"original"}) { $originaloption = 1; }
return $self;
}
sub getRelatedness
{
my $self = shift;
return undef if(!defined $self || !ref $self);
my $concept1 = shift;
my $concept2 = shift;
# set up the interface
my $interface = $self->{'interface'};
# get the minimum depth of the two concepts
my $c1_depth = $interface->findMinimumDepth($concept1);
my $c2_depth = $interface->findMinimumDepth($concept2);
if( !(defined $c1_depth) or !(defined $c2_depth)) {
return -1;
}
# find the lcses
my $lcses = $interface->findLeastCommonSubsumer($concept1, $concept2);
# get the minimum depth of the lowest lcs
my $lcs_depth = -1;
foreach my $l (@{$lcses}) {
my $ldepth = $interface->findMinimumDepth($l);
if($lcs_depth == -1) { $lcs_depth = $ldepth; }
elsif($ldepth < $lcs_depth) { $lcs_depth = $ldepth; }
}
# if the lcs depth is zero just return zero
if($lcs_depth < 0) { return -1; }
# find the shortest path between the concepts
my $l = $interface->findShortestPathLength($concept1, $concept2);
# calculate nam
my $D = $interface->depth();
my $score = log( $l * ($D-$lcs_depth) + 2 ) / log(2);
if(defined $originaloption) { return $score; }
else { return (1/$score); }
}
1;
__END__
=head1 NAME
UMLS::Similarity::nam - Perl module for computing semantic relatedness
of concepts in the Unified Medical Language System (UMLS) using the
method described by Nguyen and Al-Mubaid (2006)
=head1 CITATION
@inproceedings{NguyenA06,
title={{New ontology-based semantic similarity measure
for the biomedical domain}},
author={Nguyen, H.A. and Al-Mubaid, H.},
booktitle={Proceedings of the IEEE International Conference
on Granular Computing},
pages={623--628},
year={2006}
}
=head1 SYNOPSIS
use UMLS::Interface;
use UMLS::Similarity::nam;
my $umls = UMLS::Interface->new();
die "Unable to create UMLS::Interface object.\n" if(!$umls);
my $nam = UMLS::Similarity::nam->new($umls);
die "Unable to create measure object.\n" if(!$nam);
my $cui1 = "C0005767";
my $cui2 = "C0007634";
$ts1 = $umls->getTermList($cui1);
my $term1 = pop @{$ts1};
$ts2 = $umls->getTermList($cui2);
my $term2 = pop @{$ts2};
my $value = $nam->getRelatedness($cui1, $cui2);
print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";
=head1 DESCRIPTION
The Nguyen and Al-Mubaid measure calculates similarity by calculating
the log of two plus the product of the shortest distance between the
two concepts minus one and the depth of the taxonomy minus the depth
of the LCS. Concepts that are more similar with have a lower similarity
score than concepts that are less similar with this measure.
=head1 USAGE
The semantic relatedness modules in this distribution are built as classes
that expose the following methods:
new()
getRelatedness()
=head1 TYPICAL USAGE EXAMPLES
To create an object of the nam measure, we would have the following
lines of code in the perl program.
use UMLS::Similarity::nam;
$measure = UMLS::Similarity::nam->new($interface);
The reference of the initialized object is stored in the scalar
variable '$measure'. '$interface' contains an interface object that
should have been created earlier in the program (UMLS-Interface).
If the 'new' method is unable to create the object, '$measure' would
be undefined.
To find the semantic relatedness of the concept 'blood' (C0005767) and
the concept 'cell' (C0007634) using the measure, we would write
the following piece of code:
$relatedness = $measure->getRelatedness('C0005767', 'C0007634');
=head1 CONFIGURATION OPTION
The UMLS-Interface package takes a configuration file to determine
which sources and relations to use when obtaining the path information.
The format of the configuration file is as follows:
SAB ::
REL ::
For example, if we wanted to use the MSH vocabulary with only
the RB/RN relations, the configuration file would be:
SAB :: include MSH
REL :: include RB, RN
or
SAB :: include MSH
REL :: exclude PAR, CHD
If you go to the configuration file directory, there will
be example configuration files for the different runs that
you have performed.
For more information about the configuration options please
see the README.
=head1 SEE ALSO
perl(1), UMLS::Interface
perl(1), UMLS::Similarity(3)
=head1 CONTACT US
If you have any trouble installing and using UMLS-Similarity,
please contact us via the users mailing list :
umls-similarity@yahoogroups.com
You can join this group by going to:
http://tech.groups.yahoo.com/group/umls-similarity/
You may also contact us directly if you prefer :
Bridget T. McInnes: bthomson at cs.umn.edu
Ted Pedersen : tpederse at d.umn.edu
=head1 AUTHORS
Bridget T McInnes
Siddharth Patwardhan
Serguei Pakhomov
Ted Pedersen
=head1 COPYRIGHT AND LICENSE
Copyright 2004-2011 by Bridget T McInnes, Siddharth Patwardhan,
Serguei Pakhomov, Ying Liu and Ted Pedersen
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut